Visualisation Tools

  • Fiji - You can use virtual stacks or the BigDataViewer to navigate large datasets
  • Icy - Fiji alternative
  • ClearVolume - Fiji plugin for making pretty transparent volumes.
  • spimagine - Volume renderer
  • Fluorender - 3D volume renderer aimed at neuroscientists. Probably can’t handle large datasets.
  • VAA3D - Multi-dimensional data viewer for big datasets. Can be hard to set up but is powerful.
  • MIB - General purpose MATLAB-based viewer for quick visualisations. No big data options.
  • Knossos - Big data image annotator
  • Orbit - Image analysis tool
  • Free Imaris Viewer - Imaris now have a stripped down version that is free

Analysis Tools

  • BrainGlobe - Rich suite of tools for analysing whole-brain imaging data. This toolkit is developed at the SWC with the help of international collaborators.
  • Napari - Fast visualisation of big image data in Python. Napari really shines as a platform for building image analysis tools.
  • QuPath - Whole slide analysis
  • ABBA - Register brain slice images to the Allen Atlas.
  • SHARCQ - Register slices to the Allen Atlas atlas and perform cell quantification.
  • SHARP-Track - Register sliced brains with probe tracks to Allen Atlas. Source contains a lot of hard-coded file paths.
  • HERBS - Electrode track reconstruction from slices.

Useful stuff

Blogs

Image analysis guides

Courses

microtutor

Image acquisition or analysis references

Regular Suppliers